Each year, more than ten million new cases of cancer are diagnosed, a number that is expected to approach fifteen million by the year 2015 (Stewart, B W and Kleihues, P. (2003) World Cancer Report World Health Organization, IARC). Important for improving the quality of life and survivorship of individuals diagnosed with cancer, is the availability of new tools for the diagnosis and treatment of cancer. Currently used detection methods include imaging (CAT scan, EUS, ERCP), and histopathology, frequently involving the use of antibodies for cancer-specific markers on a biopsy specimen. Diagnosis of cancer may also involve the detection of cancer-specific markers in the serum.
The use of cancer type-specific drugs and biologics has also revolutionized the treatment of cancers. Older, non-surgical treatments typically involve powerful chemotherapeutic agents and radiotherapeutic approaches that often result in side-effects that lower the quality of life for the patient. The use of cancer tumor-type specific drugs; including antibodies, polypeptides, soluble receptors, small molecule drugs, aptamers, and polynucleotide-based reagents, has the potential to significantly improve the treatment outlook for all types of cancers, whether these treatments are used alone or in combination with existing therapies. The potential for improved treatment also increases with early detection.
The American Cancer Society has determined that breast cancer is the second leading cause of cancer death in women. Currently, there is a 1 in 33 chance that breast cancer will be responsible for a woman's death. Also according to the American Cancer Society, melanoma, which is the most deadly type of skin cancer, is increasing in frequency among the population in the U.S. In 2007, it is estimated that there will be over 59,000 new cases of melanoma diagnosed and over 8,100 deaths resulting from melanoma.
The success of available treatments for breast cancer may be enhanced by its early detection. Detection of cancer cell-specific biomarkers provides an effective screening strategy for a number of cancers. Their early detection provides not only early diagnosis, but also the ability to screen for and detect post-operative residual tumor cells, and for occult metastases, an early indicator of tumor recurrence. Early detection can thus improve survival in patients before diagnosis, while undergoing treatment, and while in remission.
In the figure, relative gene expression is shown on the Y-axis, while breast cancer tissue and normal breast tissue specimens are indicated by specimen number on the X-axis. Normal tissue specimens are labeled “Normal.” Gene expression values shown are relative to GAPDH, a housekeeping gene maintained at constant levels in all tissues. Each quantitative real time PCR was performed in duplicate, as represented by paired bars for each sample. The results show that a gene in cluster 192473 is overexpressed in eight of 19 breast cancer samples examined and in none of two normal breast cancer samples examined.
FIG. 3 shows the expression level of cluster 192473 in 2 melanoma tissues as detected by quantitative real time PCR using probes F-2, R-2 complement, and P-2 CFAM, all of which are specific to genes in cluster 192473 and described in FIG. 1.
In FIG. 3, relative gene expression is shown on the Y-axis, while melanoma cancer tissue samples are indicated by specimen number on the X-axis. Gene expression values shown are relative to GAPDH, a housekeeping gene maintained at constant levels in all tissues. Each quantitative real time PCR reaction was performed in duplicate, as represented by paired bars for each sample. The results show that a gene in cluster 192473 is overexpressed in one of two melanoma cancer samples examined.
FIG. 4 shows the expression level of cluster 192473 in seven normal heart samples; five normal kidney samples; one normal placenta sample; five normal liver samples; one normal fat samples; three normal muscle samples; and three normal adrenal gland samples, as detected by quantitative real time PCR using probes F-2, R-2 complement, and P-2 CFAM, all of which are specific to genes in cluster 192473 and described in FIG. 1. Each quantitative real time PCR was performed in duplicate, as represented by paired bars for each sample.
FIG. 5 shows an exon map, as described in FIG. 1, but providing the genomic locations of various clones assigned to cluster 800228. Each line represents the location of a nucleotide sequence, identified by a clone number, such as CLN00541308—5pv1, with a gap representing the location of the intron. The designation, “5pv1” represents the sequence identified in the first round of 5′ end sequencing. Similarly, “5pv2” represents the sequence identified in the second round of 5′ end sequencing. The designation, “3pv1” represents the sequence identified in the first round of 3′ end sequencing and “3pv2” represents the sequence identified in the second round of 3′ end sequencing. The overlap of the 5′ end sequencing and the 3′ end sequencing provided confidence that the full-length sequence of the clone had been obtained.
FIG. 6 shows the expression level of cluster 800228 in 19 breast cancer tissues and in two normal breast tissues as detected by quantitative real time PCR using probes specific to genes in cluster 800228.
In FIG. 6, relative gene expression is shown on the Y-axis, while breast cancer tissue and normal breast tissue specimens are indicated by specimen number on the X-axis. Gene expression values shown are relative to GAPDH, a housekeeping gene maintained at constant levels in all tissues. Each quantitative real time PCR was performed in duplicate, as represented by paired bars for each sample. The results show that a gene in cluster 800228 is overexpressed in 12 of 19 breast cancer samples examined and in one of two normal breast cancer samples examined.
FIG. 7 shows the expression level of cluster 800228 in seven normal heart samples; five normal kidney samples; one normal placenta sample; five normal liver samples; one normal fat samples; three normal muscle samples; and three normal adrenal gland samples as detected by quantitative real time PCR using probes specific to genes in cluster 800228. Each quantitative real time PCR was performed in duplicate, as represented by paired bars for each sample.
FIG. 8 shows an amino acid sequence alignment of the human CLN00496840 amino acid sequence, SEQ ID NO: 111 (indicated as “CLN004,” top sequence) and the corresponding chimpanzee amino acid sequence, SEQ ID NO: 165 (bottom sequence), which are encoded by nucleotide sequences assigned to cluster 800228, and represented by SEQ. ID. NOS.: 106 and 109, respectively.
FIG. 9 shows an exon map providing the genomic location of certain nucleotide sequences assigned to cluster 800634. The horizontal axis is a scaled version of the genome which considers all the introns to have equal lengths. Each line represents a sequence of a clone, CLN00156137, obtained from different rounds of sequencing. “5pv1” represents the read from the first round of 5′ end sequencing; “5pv2” represents the read from the second round of 5′ end sequencing; “3pv1” represents the first round of 3′ end sequencing; “3pv2” represents the second round of the 3′ end sequencing; “pw” represents the read from primer walking. Based on these sequencing rounds, the full length of CLN00156137 (SEQ. ID. NO.: 179) was obtained. Furthermore, the circled area depicted for CLN00154127, represents the nucleotide sequence that was amplified in the PCR analysis of gene expression of the gene of cluster 800634, as shown in the figures below.
FIG. 10 shows the expression level of cluster 800634 in 19 breast cancer tissues and in 2 normal breast tissues, and in 19 prostate cancer tissues and 3 normal prostate tissues as detected by quantitative real time PCR using probes specific to genes in cluster 800634.
In FIG. 10, relative gene expression is shown on the Y-axis, while breast cancer tissue and normal breast tissue specimens are indicated by specimen number on the right half of the X-axis. Prostate cancer and normal prostate tissues are indicated by specimen number on the left half of the X-axis. Gene expression values shown are relative to GAPDH, a housekeeping gene maintained at constant levels in all tissues. Each quantitative real time PCR was performed in duplicate, as represented by paired bars for each sample.
The results show that a gene in cluster 800634 is overexpressed in 12 of 19 breast cancer samples examined and in one of two normal breast cancer samples examined. The results also show that a gene in cluster 800634 is overexpressed in none of 19 prostate cancer samples examined and in none of three prostate cancer samples examined.
FIG. 11 shows the expression level of cluster 800634 in seven normal heart samples; five normal kidney samples; one normal placenta sample; five normal liver samples; one normal fat sample; three normal muscle samples; and three normal adrenal gland samples as detected by quantitative real time PCR using probes specific to genes in cluster 800634.
In FIG. 11, relative gene expression is shown on the Y-axis, while various normal tissue samples are indicated by specimen number on the X-axis. Gene expression values shown are relative to GAPDH, a housekeeping gene maintained at constant levels in all tissues. Each quantitative real time PCR reaction was performed in duplicate, as represented by paired bars for each sample.